Nanopore data has been generated from R10.4.1 chemistry flow cells. The reads have been basecalled in SUP mode

BioSample Accession(s)

SAMEA114263419, ERS16252358

ENA-CHECKLIST

ERC000011

organism

metagenome

collection date

2022-06-15

scientific_name

metagenome

geographic location (country and/or sea)

Denmark

ENA-LAST-UPDATE

2023-08-14

HQ MAG for uncultured Gammaproteobacteria bacterium, recovered from an environmental sample from Denmark

BioSample Accession(s)

SAMEA114814121, ERS17238988

ENA-CHECKLIST

ERC000011

binning software

MetaBAT2, GraphMB, SemiBin2, DAS Tool, mmlong2

organism

uncultured Gammaproteobacteria bacterium

broad-scale environmental context

Saltwater

assembly quality

Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better

collection date

2022-06-15

sample derived from

ERS16252358

geographic location (longitude)

11.0731

taxonomic identity marker

multi-marker approach

binning parameters

Ensemble iterative binning using coverage and kmer

completeness score

98.43

contamination score

0.34

environmental medium

not collected

geographic location (latitude)

55.677

scientific_name

uncultured Gammaproteobacteria bacterium

local environmental context

Harbours

metagenomic source

marine metagenome

project name

Microflora Danica

completeness software

CheckM2

geographic location (country and/or sea)

Denmark

isolation_source

Water

ENA-LAST-UPDATE

2023-12-07

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX11423445" alias="ena-EXPERIMENT-TAB-12-09-2023-14:26:14:009-29450" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX11423445</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-12-09-2023-14:26:14:009-29450</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS16252358">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS16252358</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA114263419</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-CHJ-R1041-MFD03250</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS16252358</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA27206554</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11423445&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11423445&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX11405086" alias="ena-EXPERIMENT-TAB-05-09-2023-18:43:51:220-5112" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX11405086</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-05-09-2023-18:43:51:220-5112</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS16252358">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS16252358</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA114263419</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-CHJ-R1041-MFD03250</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS16252358</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA27188800</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11405086&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11405086&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX11405084" alias="ena-EXPERIMENT-TAB-05-09-2023-18:43:51:219-5108" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX11405084</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-05-09-2023-18:43:51:219-5108</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS16252358">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS16252358</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA114263419</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-CHJ-R1041-MFD03250</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS16252358</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA27188800</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11405084&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11405084&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX11405085" alias="ena-EXPERIMENT-TAB-05-09-2023-18:43:51:220-5110" center_name="Center for Microbial Communities">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX11405085</PRIMARY_ID>
    <SUBMITTER_ID namespace="Center for Microbial Communities">ena-EXPERIMENT-TAB-05-09-2023-18:43:51:220-5110</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PromethION sequencing</TITLE>
  <STUDY_REF accession="ERP143702">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP143702</PRIMARY_ID>
      <SECONDARY_ID>PRJEB58634</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="ERS16252358">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS16252358</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA114263419</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LIB-CHJ-R1041-MFD03250</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS16252358</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA27188800</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11405085&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX11405085&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>